Nucleic acid sequencing, in which the order of nucleotides in a nucleic acid molecule is determined, has become ubiquitous in a wide variety of medical applications, such as biological research, genetic testing, and so forth. One type of sequencing utilized in such applications is sequencing-by-synthesis in which the order of nucleotides in a nucleic acid strand is determined by synthesizing a corresponding strand. While sequencing-by-synthesis is a high throughput method employed in many current platforms, there are several drawbacks associated with its use. For example, sequencing-by-synthesis platforms generate large volumes of sequencing data that must subsequently be processed to determine the order of the nucleotides in a given nucleic acid strand. Further, the sequencing data obtained via these methods may include a variety of errors, such as loss of phase synchrony (i.e., loss of synchronous synthesis of the identical templates), that hinder the ability to make accurate base calls. Accordingly, there exists a need for systems and methods that address these issues and enable more accurate and efficient handling of the large volumes of sequencing data obtained via the sequencing-by-synthesis platforms.